# Ene-residue - takes long **URL:** \ **Category:** HADDOCK\ **Created:** [November 15, 2021, 11:55am UTC](https://ask.bioexcel.eu/t/ene-residue-takes-long/3336 "2021-11-15T11:55:14Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![kamil](https://avatars.discourse-cdn.com/v4/letter/k/94ad74/32.png) [@kamil](https://ask.bioexcel.eu/u/kamil)\ **Post date:** [November 15, 2021, 11:55am UTC](https://ask.bioexcel.eu/t/ene-residue-takes-long/3336/1 "2021-11-15T11:55:14Z")
Dear HADDOCK community, I’m running HADDOCK2.4 locally, using qsub. The task is to dock two proteins: 800aa and 300aa to find some suggestions about their interaction. I use coarse-grained representation, 50000 structures in it0, 5000 in it1 and 5000 in it2. The point computations became inefficient is (fragment of haddock output): - BEGIN: Mon Nov 15 08:36:18 2021 - Read 5000x5000 distance matrix in 14 seconds - Writing 354 Clusters - Coverage 67.34% (3367/5000) - END: Mon Nov 15 08:36:33 2021 [14.86 seconds] Clustering in /home/project/cg\_prim\_core\_50k/run1/structures/it1/analysis DONE Check file /home/project/cg\_prim\_core\_50k/run1/structures/it1/analysis /cluster.out waiting for the ene-residue file in it1/analysis… It runs on a single CPU (but might be easily made parallel as it just writes energies between pairs of residues to a single file - the pipeline might merge several files afterwards) - does parallelization of this process makes sense? Also, does analyzing 5000 structures in it1 makes sense? Or just should I make 100’000 in it0 and then analyze 1000 in it1? I really wanted to sample the space of possibilities as I have no clues about the interaction, and the result from webserver with a limited number of structures was inconclusive. I’d be grateful for any suggestions. ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [November 15, 2021, 12:40pm UTC](https://ask.bioexcel.eu/t/ene-residue-takes-long/3336/2 "2021-11-15T12:40:41Z")
Our default sampling is 1000/200/200 or 10000/400/400 in ab-initio mode. And from time to time may-be pushing to 50000 it0 / 1000 it1 Your sampling numbers are much higher… This is of course coming at a price. Especially if you have some info to drive the docking you don’t need such high sampling. ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [November 15, 2021, 12:42pm UTC](https://ask.bioexcel.eu/t/ene-residue-takes-long/3336/3 "2021-11-15T12:42:57Z")
PS: The numbers below are actually quite efficient! clustering of 5000 models in 15s… It1 and water are the more costly parts. So not sure what you qualify as inefficient… ---
**Author:** ![kamil](https://avatars.discourse-cdn.com/v4/letter/k/94ad74/32.png) [@kamil](https://ask.bioexcel.eu/u/kamil)\ **Post date:** [November 15, 2021, 1:20pm UTC](https://ask.bioexcel.eu/t/ene-residue-takes-long/3336/4 "2021-11-15T13:20:14Z")
Inefficient in that ene-residue job, but not in terms of the development but a rather overall approach - HADDOCK runs impressively fast (I have one 128thread CPU). Maybe I should decrease it1 to 1000 since it would have a considerable dataset generated in it0 to choose from anyway. I skip water as I’m using coarse-grained {===\>} firstwater=“no”; ← when this option was on by default the procedure crashed in it1 {===\>} waterdock=false; ← wasn’t sure if I want that so disabled also. ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [November 15, 2021, 3:27pm UTC](https://ask.bioexcel.eu/t/ene-residue-takes-long/3336/5 "2021-11-15T15:27:23Z")
> Inefficient in that ene-residue job, but not in terms of the development but a rather overall approach - HADDOCK runs impressively fast (I have one 128thread CPU). I would simply skip that part, unless you need to extract those metrics. For sure for ab-initio docking it is very inefficient as you are basically calculating it for the entire surface. Setting the analysis to clustering only will be much more efficient. > I skip water as I’m using coarse-grained > {===\>} firstwater=“no”; ← when this option was on by default the procedure crashed in it1 Would be strange that it crashes at it1 since it is only performed after it1… > {===\>} waterdock=false; ← wasn’t sure if I want that so disabled also. You don’t want it - trust the default settings… And not possible with CG anyway ---
**Author:** ![kamil](https://avatars.discourse-cdn.com/v4/letter/k/94ad74/32.png) [@kamil](https://ask.bioexcel.eu/u/kamil)\ **Post date:** [November 15, 2021, 4:08pm UTC](https://ask.bioexcel.eu/t/ene-residue-takes-long/3336/6 "2021-11-15T16:08:40Z")
> [@amjjbonvin](#): > > Would be strange that it crashes at it1 since it is only performed after it1… Ah, sorry, yes, it crashed for smaller test coarse grained run, after it1, yes.